Microbial Informatics

Lecture 02

Patrick D. Schloss, PhD (microbialinformatics.github.io)
Department of Microbiology & Immunology

"Markdown is a text-to-HTML conversion tool for web writers. Markdown allows you to write using an easy-to-read, easy-to-write plain text format, then convert it to structurally valid XHTML (or HTML)." - John Gruber
The advantage is that you can read it as a text document and it will make sense and you can use conversion software to generate other file formats including html, pdf, docx
Can be rendered using:
- A Perl script from Gruber
- RStudio

"R Markdown is an authoring format that enables easy creation of dynamic documents, presentations, and reports from R. It combines the core syntax of markdown (an easy-to-write plain text format) with embedded R code chunks that are run so their output can be included in the final document. R Markdown documents are fully reproducible (they can be automatically regenerated whenever underlying R code or data changes)." - RStudio website
Keys...
- Ability to format text
- Imbed R code and output as chunks or inline

plot of chunk unnamed-chunk-1

Let me pick a random number between 1 and 10.
Hmmm, I pick 5
5 squared is 25
All of the numbers (after 1 and 10) were generated within R
The dynamic component is that you use R packages to allow a user to set the min and max values to bound your pick

The chunks and inline approaches are implemented using an R package called knitr
We will talk about knitr later when we start digging into R's syntax
Documenation and a book (written in knitr) can be found on Yi Hui's website

An R markdown "cheat sheet" is available for you to download and print from rstudio.com
Other documentation, examples, tutorials are available at rmarkdown.rstudio.com
- You can use existing document templates
- You can design your own report templates
- Possible to insert paper references
- There's a lot more there
We will be using R markdown tomorrow as part of the exercise